scholarly journals Engineered inter-species amino acid cross-feeding increases population evenness in a synthetic bacterial consortium

2018 ◽  
Author(s):  
Marika Ziesack ◽  
Travis Gibson ◽  
John K.W. Oliver ◽  
Andrew M. Shumaker ◽  
Bryan B. Hsu ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Consortium ◽  
Microbial Interactions ◽  
Environmental Benefits ◽  
Microbial Consortia ◽  
Positive Interactions ◽  
Complex Environments ◽  
Bacterial Consortia ◽  
Health And Disease ◽  
Antagonistic Interactions

AbstractIn nature, microbes interact antagonistically, neutrally or beneficially. To shed light on the effects of positive interactions in microbial consortia we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wildtype consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.ImportanceMicrobial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortia function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

scholarly journals Engineered Interspecies Amino Acid Cross-Feeding Increases Population Evenness in a Synthetic Bacterial Consortium

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Marika Ziesack ◽  
Travis Gibson ◽  
John K. W. Oliver ◽  
Andrew M. Shumaker ◽  
Bryan B. Hsu ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Bacterial Consortium ◽  
Microbial Interactions ◽  
Environmental Benefits ◽  
Microbial Consortia ◽  
Positive Interactions ◽  
Complex Environments ◽  
Bacterial Consortia ◽  
Health And Disease ◽  
Antagonistic Interactions

ABSTRACT In nature, microbes interact antagonistically, neutrally, or beneficially. To shed light on the effects of positive interactions in microbial consortia, we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wild-type consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments, including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments. IMPORTANCE Microbial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment, and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortium function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us in deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

scholarly journals Raw Cow Milk Bacterial Consortium as Bioindicator of Circulating Anti-Microbial Resistance (AMR)

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2378
Author(s):  
Cristian Piras ◽  
Viviana Greco ◽  
Enrico Gugliandolo ◽  
Alessio Soggiu ◽  
Bruno Tilocca ◽  
...  
Keyword(s):  
Ecological Niche ◽  
Bacterial Species ◽  
Raw Milk ◽  
Bacterial Consortium ◽  
Cow Milk ◽  
Milk Analysis ◽  
Animal Products ◽  
Bacterial Consortia ◽  
Expression Of Genes ◽  
Ecological Pressure

The environment, including animals and animal products, is colonized by bacterial species that are typical and specific of every different ecological niche. Natural and human-related ecological pressure promotes the selection and expression of genes related to antimicrobial resistance (AMR). These genes might be present in a bacterial consortium but might not necessarily be expressed. Their expression could be induced by the presence of antimicrobial compounds that could originate from a given ecological niche or from human activity. In this work, we applied (meta)proteomics analysis of bacterial compartment of raw milk in order to obtain a method that provides a measurement of circulating AMR involved proteins and gathers information about the whole bacterial composition. Results from milk analysis revealed the presence of 29 proteins/proteoforms linked to AMR. The detection of mainly β-lactamases suggests the possibility of using the milk microbiome as a bioindicator for the investigation of AMR. Moreover, it was possible to achieve a culture-free qualitative and functional analysis of raw milk bacterial consortia.

scholarly journals Establishing and Optimizing a Bacterial Consortia for Effective Biodegradation of Petroleum Contaminants: Advancing Classical Microbiology via Experimental and Mathematical Approach

Water ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 3311
Author(s):  
Baichun Wu ◽  
Jingmin Deng ◽  
Hao Niu ◽  
Jiahao Liang ◽  
Muhammad Arslan ◽  
...  
Keyword(s):  
Partial Correlation ◽  
High Efficiency ◽  
Bacterial Species ◽  
Rhodococcus Erythropolis ◽  
Bacterial Consortium ◽  
Bacterial Strains ◽  
Bacterial Consortia ◽  
Orthogonal Experiments ◽  
Petroleum Contaminants ◽  
Different Strains

In classical microbiology, developing a high-efficiency bacterial consortium is a great challenge for faster biodegradation of petroleum contaminants. In this study, a systematic experimental and mathematical procedure was adopted to establish a bacterial consortium for the effective biodegradation of heavy oil constituents. A total of 27 bacterial consortia were established as per orthogonal experiments, using 8 petroleum-degrading bacterial strains. These bacteria were closer phylogenetic relatives of Brevundimonas sp. Tibet-IX23 (Y1), Bacillus firmus YHSA15, B. cereus MTCC 9817, B. aquimaris AT8 (Y2, Y6 and Y7), Pseudomonas alcaligenes NBRC (Y3), Microbacterium oxydans CV8.4 (Y4), Rhodococcus erythropolis SBUG 2052 (Y5), and Planococcus sp. Tibet-IX21 (Y8), and were used in different combinations. Partial correlation analysis and a general linear model hereafter were applied to investigate interspecific relationships among different strains and consortia. The Y1 bacterial species showed a remarkable synergy, whereas Y3, Y4, and Y6 displayed a strong antagonism in all consortia. Inoculation ratios of different strains significantly influenced biodegradation. An optimal consortium was constructed with Y1, Y2, Y5, Y7, and Y8, which revealed maximum degradation of 11.238 mg/mL OD600 for oil contaminants. This study provides a line of evidence that a functional consortium can be established by mathematical models for improved bioremediation of petroleum-contaminated environment.

scholarly journals Combining Culture-Dependent and Independent Approaches for the Optimization of Epoxiconazole and Fludioxonil-Degrading Bacterial Consortia

2021 ◽  
Vol 9 (10) ◽  
pp. 2109
Author(s):  
Diogo Alexandrino ◽  
Ana Mucha ◽  
Maria Paola Tomasino ◽  
C. Marisa R. Almeida ◽  
Maria Carvalho
Keyword(s):  
Agricultural Soil ◽  
Enrichment Culture ◽  
Bacterial Species ◽  
The Other ◽  
Microbial Consortia ◽  
Bacterial Isolates ◽  
Bacterial Strains ◽  
Bacterial Consortia ◽  
First Time ◽  
Culture Dependent

Epoxiconazole (EPO) and fludioxonil (FLU) are two widely used fluorinated pesticides known to be highly persistent and with high ecotoxicological potential, turning them into pollutants of concern. This work aimed to optimize two degrading bacterial consortia, previously obtained from an agricultural soil through enrichment with EPO and FLU, by characterizing the contribution of their corresponding bacterial isolates to the biodegradation of these pesticides using both culture-dependent and independent methodologies. Results showed that a co-culture of the strains Hydrogenophaga eletricum 5AE and Methylobacillus sp. 8AE was the most efficient in biodegrading EPO, being able to defluorinate ca. 80% of this pesticide in 28 days. This catabolic performance is likely the result of a commensalistic cooperation, in which H. eletricum may be the defluorinating strain and Methylobacillus sp. may assume an accessory, yet pivotal, catabolic role. Furthermore, 16S rRNA metabarcoding analysis revealed that these strains represent a minority in their original consortium, showing that the biodegradation of EPO can be driven by less abundant phylotypes in the community. On the other hand, none of the tested combinations of bacterial strains showed potential to biodegrade FLU, indicating that the key degrading strains were not successfully isolated from the original enrichment culture. Overall, this work shows, for the first time, the direct involvement of two bacterial species, namely H. eletricum and Methylobacillus sp., in the biodegradation of EPO, while also offering insight on how they might cooperate to accomplish this process. Moreover, the importance of adequate culture-dependent approaches in the engineering of microbial consortia for bioremediation purposes is also emphasized.

scholarly journals Quantifying multi-species microbial interactions in the larval zebrafish gut

2020 ◽  
Author(s):  
Deepika Sundarraman ◽  
Edouard A. Hay ◽  
Dylan M. Martins ◽  
Drew S. Shields ◽  
Noah L. Pettinari ◽  
...  
Keyword(s):  
Species Interactions ◽  
Bacterial Species ◽  
Higher Order ◽  
Microbial Interactions ◽  
Microbial Composition ◽  
Intestinal Microbes ◽  
Larval Zebrafish ◽  
Species Abundances ◽  
Health And Disease ◽  
Multiple Species

AbstractThe microbial communities resident in animal intestines are composed of multiple species that together play important roles in host development, health and disease. Due to the complexity of these communities and the difficulty of characterizing them in situ, the determinants of microbial composition remain largely unknown. Further, it is unclear for many multi-species consortia whether their species-level makeup can be predicted based on an understanding of pairwise species interactions, or whether higher-order interactions are needed to explain emergent compositions. To address this, we examine commensal intestinal microbes in larval zebrafish, initially raised germ-free to allow introduction of controlled combinations of bacterial species. Using a dissection and plating assay, we demonstrate the construction of communities of one to five bacterial species and show that the outcomes from the two-species competitions fail to predict species abundances in more complex communities. With multiple species present, inter-bacterial interactions become weaker and more cooperative, suggesting that higher-order interactions in the vertebrate gut may stabilize complex communities.

scholarly journals Biodegradation of a Complex Phenolic Industrial Stream by Bacterial Strains Isolated from Industrial Wastewaters

Processes ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1964
Author(s):  
Alejandra Bartolomé ◽  
Gema Rodríguez-Moro ◽  
Juan-Luis Fuentes ◽  
Mariana Lopes ◽  
Juana Frontela ◽  
...  
Keyword(s):  
Phenolic Compounds ◽  
Bacterial Species ◽  
Treatment Plant ◽  
Bacterial Consortium ◽  
Molecular Techniques ◽  
Bacterial Strains ◽  
Batch Mode ◽  
Bacterial Consortia ◽  
Massive Sequencing ◽  
Repeated Batch

Molecular and metabolomic tools were used to design and understand the biodegradation of phenolic compounds in real industrial streams. Bacterial species were isolated from an industrial wastewater treatment plant of a phenol production factory and identified using molecular techniques. Next, the biodegradation potential of the most promising strains was analyzed in the presence of a phenolic industrial by-product containing phenol, alfa-methylstyrene, acetophenone, 2-cumylphenol, and 4-cumylphenol. A bacterial consortium comprising Pseudomonas and Alcaligenes species was assessed for its ability to degrade phenolic compounds from the phenolic industrial stream (PS). The consortium adapted itself to the increasing levels of phenolic compounds, roughly up to 1750 ppm of PS; thus, becoming resistant to them. In addition, the consortium exhibited the ability to grow in the presence of PS in repeated batch mode processes. Results from untargeted metabolomic analysis of the culture medium in the presence of PS suggested that bacteria transformed the toxic phenolic compounds into less harmful molecules as a survival mechanism. Overall, the study demonstrates the usefulness of massive sequencing and metabolomic tools in constructing bacterial consortia that can efficiently biodegrade complex PS. Furthermore, it improves our understanding of their biodegradation capabilities.

scholarly journals Gut Homeostasis; Microbial Cross Talks in Health and Disease Management

2021 ◽  
Vol 9 (3) ◽  
pp. 1017-1045
Author(s):  
Gauri S Khatri ◽  
Christine Kurian ◽  
Asha Anand ◽  
Paari KA
Keyword(s):  
Gastrointestinal Diseases ◽  
Bacterial Consortium ◽  
Microbial Interactions ◽  
Intestinal Homeostasis ◽  
Health And Disease ◽  
Inflammatory Bowel ◽  
Populated Region ◽  
And Function

The human gut is a densely populated region comprising a diverse collection of microorganisms. The number, type and function of the diverse gut microbiota vary at different sites along the entire gastrointestinal tract. Gut microbes regulate signaling and metabolic pathways through microbial cross talks. Host and microbial interactions mutually contribute for intestinal homeostasis. Rapid shift or imbalance in the microbial community disrupts the equilibrium or homeostatic state leading to dysbiosis and causes many gastrointestinal diseases viz., Inflammatory Bowel Disease, Obesity, Type 2 diabetes, Metabolic endotoxemia, Parkinson’s disease and Fatty liver disease etc. Intestinal homeostasis has been confounded by factors that disturb the balance between eubiosis and dysbiosis. This review correlates the consequences of dysbiosis with the incidence of various diseases. Impact of microbiome and its metabolites on various organs such as liver, brain, kidney, large intestine, pancreas etc are discussed. Furthermore, the role of therapeutic approaches such as ingestion of nutraceuticals (probiotics, prebiotics and synbiotics), Fecal Microbial Treatment, Phage therapy and Bacterial consortium treatment in restoring the eubiotic state is elaborately reviewed.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

scholarly journals Temporal Stability and Biodiversity of Two Complex Antilisterial Cheese-Ripening Microbial Consortia

2003 ◽  
Vol 69 (7) ◽  
pp. 4012-4018 ◽  
Author(s):  
Ariel Maoz ◽  
Ralf Mayr ◽  
Siegfried Scherer
Keyword(s):  
Species Composition ◽  
Bacterial Species ◽  
Temporal Stability ◽  
Individual Characteristics ◽  
Microbial Consortia ◽  
Cheese Ripening ◽  
Safe Food ◽  
The Stability ◽  
The Individual ◽  
First Time

ABSTRACT The temporal stability and diversity of bacterial species composition as well as the antilisterial potential of two different, complex, and undefined microbial consortia from red-smear soft cheeses were investigated. Samples were collected twice, at 6-month intervals, from each of two food producers, and a total of 400 bacterial isolates were identified by Fourier-transform infrared spectroscopy and 16S ribosomal DNA sequence analysis. Coryneform bacteria represented the majority of the isolates, with certain species being predominant. In addition, Marinolactobacillus psychrotolerans, Halomonas venusta, Halomonas variabilis, Halomonas sp. (106 to 107 CFU per g of smear), and an unknown, gram-positive bacterium (107 to 108 CFU per g of smear) are described for the first time in such a consortium. The species composition of one consortium was quite stable over 6 months, but the other consortium revealed less diversity of coryneform species as well as less stability. While the first consortium had a stable, extraordinarily high antilisterial potential in situ, the antilisterial activity of the second consortium was lower and decreased with time. The cause for the antilisterial activity of the two consortia remained unknown but is not due to the secretion of soluble, inhibitory substances by the individual components of the consortium. Our data indicate that the stability over time and a potential antilisterial activity are individual characteristics of the ripening consortia which can be monitored and used for safe food production without artificial preservatives.

Characterization of a designed synthetic autotrophic–heterotrophic consortia for fixing CO2 without light

RSC Advances ◽  
2016 ◽  
Vol 6 (81) ◽  
pp. 78161-78169 ◽  
Author(s):  
Jiajun Hu ◽  
Yiyun Xue ◽  
Jixiang Li ◽  
Lei Wang ◽  
Shiping Zhang ◽  
...  
Keyword(s):  
Microbial Interactions ◽  
Microbial Consortia ◽  
Synthetic Microbial Consortia

CO2 fixation efficiency of the devised synthetic microbial consortia with both autotrophic–autotrophic and autotrophic–heterotrophic microbial interactions were higher than the sum of theoretical CO2 fixation efficiency of the microbial components.

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